Molecular Simulation of the Impact of Defects on Electrolyte Intrusion in Zeolites.

We have investigated through molecular simulation the intrusion of electrolytes in two representative pure-silica zeolites, silicalite-1 and chabazite, in which point defects were introduced in varying amounts. We distinguish between two types of defects, considering either "weak" or "strong" silanol nest defects, resulting in different hydration behaviors. In the presence of weak defects, the hydration process occurs through a homogeneous nucleation process, while with strong defects, we observe an initial adsorption followed by a filling of the nanoporous volume at a higher pressure. However, we show that electrolytes do not penetrate the zeolites, and these defects appear to have only marginal influence on the thermodynamics of electrolyte intrusion. While replacing pure water by the electrolyte solution shifts the intrusion pressure toward higher values because of the drop of water saturation vapor pressure, an increase in hydrophilicity of the framework due to point defects has the opposite effect, showing that controlling the amount of defects in zeolites is crucial for storage energy applications.

New Growth-Related Features of Wheat Grain Pericarp Revealed by Synchrotron-Based X-ray Micro-Tomography and 3D Reconstruction.

Wheat (Triticum aestivum L.) is one of the most important crops as it provides 20% of calories and proteins to the human population. To overcome the increasing demand in wheat grain production, there is a need for a higher grain yield, and this can be achieved in particular through an increase in the grain weight. Moreover, grain shape is an important trait regarding the milling performance. Both the final grain weight and shape would benefit from a comprehensive knowledge of the morphological and anatomical determinism of wheat grain growth. Synchrotron-based phase-contrast X-ray microtomography (X-ray µCT) was used to study the 3D anatomy of the growing wheat grain during the first developmental stages. Coupled with 3D reconstruction, this method revealed changes in the grain shape and new cellular features. The study focused on a particular tissue, the pericarp, which has been hypothesized to be involved in the control of grain development. We showed considerable spatio-temporal diversity in cell shape and orientations, and in tissue porosity associated with stomata detection. These results highlight the growth-related features rarely studied in cereal grains, which may contribute significantly to the final grain weight and shape.

Alchemical Osmostat for Monte Carlo Simulation: Sampling Aqueous Electrolyte Solution in Open Systems.

Molecular simulations involving electrolytes are usually performed at a fixed amount of salt ions in the simulation box, reproducing macroscopic concentration. Although this statement is valid in the bulk, the concentration of an electrolyte confined in nanoporous materials such as MOFs or zeolites is greatly affected and remains a priori unknown. The nanoporous material in equilibrium with the bulk electrolyte exchange water and ions at a given chemical potential Δµ in the semi-grand-canonical ensemble, that must be calibrated in order to determine the concentration in the nanoporous material. In this work, we propose an algorithm based on nonequilibrium candidate Monte Carlo (NCMC) moves to ultimately perform MC simulations in contact with a saline reservoir. First, we adapt the Widom insertion technique to calibrate the chemical potential by alchemically transmuting water molecules into ions by using NCMC moves. The chemical potential defines a Monte Carlo osmostat in the semi-grand-constant volume and temperature ensemble (Δµ, N, V, T) to be added in a Monte Carlo simulation where the number of ions fluctuates. In order to validate the method, we adapted the NCMC move to determine the free energy of water solvation and subsequently explore thermodynamics of electrolyte solvation at infinite dilution in water. Finally, we implemented the osmostat in MC simulations initialized with bulk water that are driven toward electrolyte solutions of similar concentration as the saline reservoir. Our results demonstrate that alchemical osmostat for MC simulation is a promising tool for use to sample electrolyte insertion in nanoporous materials.

[Rosai-Dorfman-Destombes disease with a misleading laryngeal presentation]. / Une maladie de Rosai­Dorfman­Destombes de présentation laryngée trompeuse.

Rosai-Dorfman-Destombes disease is a rare non-Langerhansian cell histiocytosis characterized by the accumulation of large activated histiocytes in the affected tissues with images of emperipolesis. The diagnosis is not really problematic in the classical forms, with a lymph node presentation, whose histology is very suggestive. However, it can be much more difficult in the extra-nodal forms, which are misleading in both their clinical and histological presentation. We report here a case illustrating this diagnostic difficulty. Firstly, clinically, the disease was revealed by an unusual laryngeal location, responsible for acute obstructive respiratory distress and requiring urgent surgical management. Secondly, histologically, the diagnosis was not evoked in the first instance by analysis of the laryngeal lesion. Indeed, there was a not specific appearing polymorphic infiltrate, associating small lymphocytes, plasma cells and numerous histiocytes, without evidence for a lymphoma after immunohistochemistry and lymphocyte clonality analysis. However, after re-examination of the slides, the histiocytes sometimes appeared large or xanthomised and have a PS100+, CD1a-, langerhine- phenotype, with rare images of emperipolesis. These aspects finally suggested the diagnosis of Rosai-Dorfman-Destombes disease, then confirmed by a cervical lymph node biopsy showing characteristic histological features. Simultaneously, NGS analysis of the laryngeal lesion showed a mutation in the MAP2K1 gene, in accordance with the diagnosis. The patient was treated with revlimid and dexamethasone for 6 months, with complete remission, and is currently undergoing maintenance treatment with revlimid.

Spatial correlation of water distribution and fine structure of arabinoxylans in the developing wheat grain.

This study was to investigate the distribution of water and arabinoxylan structures in growing wheat grain using two complementary imaging techniques, magnetic resonance microimaging (µMRI) and mass spectrometry imaging (MSI). µMRI showed an inhomogeneous water distribution, particularly at early stages. This heterogeneity revealed histological differences that corresponded, within the limits of resolution of µMRI, to tissues with specific physiological functions, including the vascular bundles, the cavity and the endosperm periphery. All of these tissues had a higher water content than the central endosperm. MSI revealed distinct xylan structures in these regions with high levels of Araf substitution around the cavity and acetylated xylans concentrated at the endosperm periphery. For the first time, acetylation and Araf substitution of arabinoxylans were found by image processing to spatially correlate with water distribution in planta. Acetylation and Araf substitution of xylans, which alter chain-chain interactions and increase wall porosity, decreased as the grain matured.

The endosperm cavity of wheat grains contains a highly hydrated gel of arabinoxylan.

Cereal grains provide a substantial part of the calories for humans and animals. The main quality determinants of grains are polysaccharides (mainly starch but also dietary fibers such as arabinoxylans, mixed-linkage glucans) and proteins synthesized and accumulated during grain development in a specialized storage tissue: the endosperm. In this study, the composition of a structure localized at the interface of the vascular tissues of the maternal plant and the seed endosperm was investigated. This structure is contained in the endosperm cavity where water and nutrients are transferred to support grain filling. While studying the wheat grain development, the cavity content was found to autofluoresce under UV light excitation. Combining multispectral analysis, Fourier-Transform infrared spectroscopy, immunolabeling and laser-dissection coupled with wet chemistry, we identified in the cavity arabinoxylans and hydroxycinnamic acids. The cavity content forms a "gel" in the developing grain, which persists in dry mature grain and during subsequent imbibition. Microscopic magnetic resonance imaging revealed that the gel is highly hydrated. Our results suggest that arabinoxylans are synthesized by the nucellar epidermis, released in the cavity where they form a highly hydrated gel which might contribute to regulate grain hydration.

The TaCslA12 gene expressed in the wheat grain endosperm synthesizes wheat-like mannan when expressed in yeast and Arabidopsis.

Mannan is a class of cell wall polysaccharides widespread in the plant kingdom. Mannan structure and properties vary according to species and organ. The cell walls of cereal grains have been extensively studied due to their role in cereal processing and to their beneficial effect on human health as dietary fiber. Recently, we showed that mannan in wheat (Triticum aestivum) grain endosperm has a linear structure of ß-1,4-linked mannose residues. The aim of this work was to study the biosynthesis and function of wheat grain mannan. We showed that mannan is deposited in the endosperm early during grain development, and we identified candidate mannan biosynthetic genes expressed in the endosperm. The functional study in wheat was unsuccessful therefore our best candidate genes were expressed in heterologous systems. The endosperm-specificTaCslA12 gene expressed in Pichia pastoris and in an Arabidopsis thaliana mutant depleted in glucomannan led to the production of wheat-like linear mannan lacking glucose residues and with moderate acetylation. Therefore, this gene encodes a mannan synthase and is likely responsible for the synthesis of wheat endosperm mannan.

Challenging the putative structure of mannan in wheat (Triticum aestivum) endosperm.

In wheat endosperm, mannan, is poorly documented. Nevertheless, this hemicellulosic polysaccharide might have a determinant role in wheat grain development since, in Arabidopsis thaliana, mutants with a reduced amount of mannan show an altered seed development. In order to gain knowledge about mannan in wheat, we have determined its biochemical structure in wheat endosperm where mannose content is about 0.2% (dry weight basis). We developed a method of enzymatic fingerprinting and isolated mannan-enriched fractions to decipher its fine structure. Although it is widely accepted that the class of mannan present in grass cell walls is glucomannan, our data indicate that, in wheat endosperm, this hemicellulose is only represented by short unsubstituted chains of 1,4 linked D-mannose residues and is slightly acetylated. Our study provides information regarding the interactions of mannan with other cell wall components and help to progress towards the understanding of monocot cell wall architecture and the mannan synthesis in wheat endosperm.

Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development.

BACKGROUND: Wheat is one of the most important staple source in the world for human consumption, animal feed and industrial raw materials. To deal with the global and increasing population demand, enhancing crop yield by increasing the final weight of individual grain is considered as a feasible solution. Morphometric analysis of wheat grain plays an important role in tracking and understanding developmental processes by assessing potential impacts on grains properties, size and shape that are major determinants of final grain weight. X-ray micro computed tomography (µCT) is a very powerful non-invasive imaging tool that is able to acquire 3D images of an individual grain, enabling to assess the morphology of wheat grain and of its different compartments. Our objective is to quantify changes of morphology during growth stages of wheat grain from 3D µCT images. METHODS: 3D µCT images of wheat grains were acquired at various development stages ranging from 60 to 310 degree days after anthesis. We developed robust methods for the identification of outer and inner tissues within the grains, and the extraction of morphometric features using 3D µCT images. We also developed a specific workflow for the quantification of the shape of the grain crease. RESULTS: The different compartments of the grain could be semi-automatically segmented. Variations of volumes of the compartments adequately describe the different stages of grain developments. The evolution of voids within wheat grain reflects lysis of outer tissues and growth of inner tissues. The crease shape could be quantified for each grain and averaged for each stage of development, helping us understand the genesis of the grain shape. CONCLUSION: This work shows that µCT acquisitions and image processing methodologies are powerful tools to extract morphometric parameters of developing wheat grain. The results of quantitative analysis revealed remarkable features of wheat grain growth. Further work will focus on building a computational model of wheat grain growth based on real 3D imaging data.

Multi-excitation hyperspectral autofluorescence imaging for the exploration of biological samples.

Many plant tissues can be observed thanks to autofluorescence of their cell wall components. Hyperspectral autofluorescence imaging using confocal microscopy is a fast and efficient way of mapping fluorescent compounds in samples with a high spatial resolution. However a huge spectral overlap is observed between molecular species. As a consequence, a new data analysis approach is needed in order to fully exploit the potential of this spectroscopic technique and extract unbiased chemical information about complex biological samples. The objective of this work is to evaluate multi-excitation hyperspectral autofluorescence imaging to identify biological components in wheat grains during their development through their spectral profiles and corresponding contribution maps using Multivariate Curve Resolution - Alternating Least-Squares (MCR-ALS), a signal unmixing algorithm under proper constraints. For this purpose two different scenarios are used: 1) analyzing the total spectral domain of data sets using MCR-ALS under non negativity constraint in both spectral and spatial modes; 2) analyzing a reduced spectral domain of data sets using MCR-ALS under non negativity in both modes and trilinearity constraint in spectral mode. Considering the original instrumental setup and our data analysis approach, we will demonstrate that extracted contribution maps and spectral profiles of constituents can provide complementary information used to identify molecules in complex biological samples.

Ferulate and lignin cross-links increase in cell walls of wheat grain outer layers during late development.

Important biological, nutritional and technological roles are attributed to cell wall polymers from cereal grains. The composition of cell walls in dry wheat grain has been well studied, however less is known about cell wall deposition and modification in the grain outer layers during grain development. In this study, the composition of cell walls in the outer layers of the wheat grain (Triticum aestivum Recital cultivar) was investigated during grain development, with a focus on cell wall phenolics. We discovered that lignification of outer layers begins earlier than previously reported and long before the grain reaches its final size. Cell wall feruloylation increased in development. However, in the late stages, the amount of ferulate releasable by mild alkaline hydrolysis was reduced as well as the yield of lignin-derived thioacidolysis monomers. These reductions indicate that new ferulate-mediated cross-linkages of cell wall polymers appeared as well as new resistant interunit bonds in lignins. The formation of these additional linkages more specifically occurred in the outer pericarp. Our results raised the possibility that stiffening of cell walls occur at late development stages in the outer pericarp and might contribute to the restriction of the grain radial growth.

Structure and Dynamics of Water Confined in Imogolite Nanotubes.

We have studied the properties of water adsorbed inside nanotubes of hydrophilic imogolite, an aluminum silicate clay mineral, by means of molecular simulations. We used a classical force field to describe the water and the flexible imogolite nanotube and validated it against the data obtained from first-principles molecular dynamics. With it, we observe a strong structuration of the water confined in the nanotube, with specific adsorption sites and a distribution of hydrogen bond patterns. The combination of number of adsorption sites, their geometry, and the preferential tetrahedral hydrogen bonding pattern of water leads to frustration and disorder. We further characterize the dynamics of the water, as well as the hydrogen bonds formed between water molecules and the nanotube, which is found to be more than 1 order of magnitude longer than water-water hydrogen bonds.

Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent.

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer-solvent interactions can lead to drastically different behavior of the polymer-surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface.

Forced intrusion of water and aqueous solutions in microporous materials: from fundamental thermodynamics to energy storage devices.

We review the high pressure forced intrusion studies of water in hydrophobic microporous materials such as zeolites and MOFs, a field of research that has emerged some 15 years ago and is now very active. Many of these studies are aimed at investigating the possibility of using these systems as energy storage devices. A series of all-silica zeolites (zeosil) frameworks were found suitable for reversible energy storage because of their stability with respect to hydrolysis after several water intrusion-extrusion cycles. Several microporous hydrophobic zeolite imidazolate frameworks (ZIFs) also happen to be quite stable and resistant towards hydrolysis and thus seem very promising for energy storage applications. Replacing pure water by electrolyte aqueous solutions enables to increase the stored energy by a factor close to 3, on account of the high pressure shift of the intrusion transition. In addition to the fact that aqueous solutions and microporous silica materials are environmental friendly, these systems are thus becoming increasingly interesting for the design of new energy storage devices. This review also addresses the theoretical approaches and molecular simulations performed in order to better understand the experimental behavior of nano-confined water. Molecular simulation studies showed that water condensation takes place through a genuine first-order phase transition, provided that the interconnected pores structure is 3-dimensional and sufficiently open. In an extreme confinement situations such as in ferrierite zeosil, condensation seem to take place through a continuous supercritical crossing from a diluted to a dense fluid, on account of the fact that the first-order transition line is shifted to higher pressure, and the confined water critical point is correlatively shifted to lower temperature. These molecular simulation studies suggest that the most important features of the intrusion/extrusion process can be understood in terms of equilibrium thermodynamics considerations.

Kinetic Accessibility of Porous Material Adsorption Sites Studied through the Lattice Boltzmann Method.

We present here a computational model based on the lattice Boltzmann scheme to investigate the accessibility of active adsorption sites in hierarchical porous materials to adsorbates in a flowing liquid. By studying the transport and adsorption of tracers after they enter the pore space of the virtual sample, we characterize their kinetics as they pass through the pore space and adsorb on the solid-liquid interface. The model is validated on simple geometries with a known analytical solution. We then use it to investigate the influence of regular grooves or disordered roughness on the walls of a slit pore geometry, looking at the impact on adsorption and transport. In particular, we highlight the importance of adsorption site accessibility, which depends on the shape and connectivity of the pore space as well as the fluid flow profile and velocity.

Transport and adsorption under liquid flow: the role of pore geometry.

We study here the interplay between transport and adsorption in porous systems with complex geometries under fluid flow. Using a lattice Boltzmann scheme extended to take into account the adsorption at solid/fluid interfaces, we investigate the influence of pore geometry and internal surface roughness on the efficiency of fluid flow and the adsorption of molecular species inside the pore space. We show how the occurrence of roughness on pore walls acts effectively as a modification of the solid/fluid boundary conditions, introducing slippage at the interface. We then compare three common pore geometries, namely honeycomb pores, inverse opal, and materials produced by spinodal decomposition. Finally, we quantify the influence of those three geometries on fluid transport and tracer adsorption. This opens perspectives for the optimization of materials' geometries for applications in dynamic adsorption under fluid flow.

Developing Pericarp of Maize: A Model to Study Arabinoxylan Synthesis and Feruloylation.

Cell walls are comprised of networks of entangled polymers that differ considerably between species, tissues and developmental stages. The cell walls of grasses, a family that encompasses major crops, contain specific polysaccharide structures such as xylans substituted with feruloylated arabinose residues. Ferulic acid is involved in the grass cell wall assembly by mediating linkages between xylan chains and between xylans and lignins. Ferulic acid contributes to the physical properties of cell walls, it is a hindrance to cell wall degradability (thus biomass conversion and silage digestibility) and may contribute to pest resistance. Many steps leading to the formation of grass xylans and their cross-linkages remain elusive. One explanation might originate from the fact that many studies were performed on lignified stem tissues. Pathways leading to lignins and feruloylated xylans share several steps, and lignin may impede the release and thus the quantification of ferulic acid. To overcome these difficulties, we used the pericarp of the maize B73 line as a model to study feruloylated xylan synthesis and crosslinking. Using Fourier-transform infra-red spectroscopy and biochemical analyses, we show that this tissue has a low lignin content and is composed of approximately 50% heteroxylans and approximately 5% ferulic acid. Our study shows that, to date, maize pericarp contains the highest level of ferulic acid reported in plant tissue. The detection of feruloylated xylans with a polyclonal antibody shows that the occurrence of these polysaccharides is developmentally regulated in maize grain. We used the genomic tools publicly available for the B73 line to study the expression of genes within families involved or suggested to be involved in the phenylpropanoid pathway, xylan formation, feruloylation and their oxidative crosslinking. Our analysis supports the hypothesis that the feruloylated moiety of xylans originated from feruloylCoA and is transferred by a member of the BAHD acyltransferase family. We propose candidate genes for functional characterization that could subsequently be targeted for grass crop breeding.

Mutation in Brachypodium caffeic acid O-methyltransferase 6 alters stem and grain lignins and improves straw saccharification without deteriorating grain quality.

Cereal crop by-products are a promising source of renewable raw material for the production of biofuel from lignocellulose. However, their enzymatic conversion to fermentable sugars is detrimentally affected by lignins. Here the characterization of the Brachypodium Bd5139 mutant provided with a single nucleotide mutation in the caffeic acid O-methyltransferase BdCOMT6 gene is reported. This BdCOMT6-deficient mutant displayed a moderately altered lignification in mature stems. The lignin-related BdCOMT6 gene was also found to be expressed in grains, and the alterations of Bd5139 grain lignins were found to mirror nicely those evidenced in stem lignins. The Bd5139 grains displayed similar size and composition to the control. Complementation experiments carried out by introducing the mutated gene into the AtCOMT1-deficient Arabidopsis mutant demonstrated that the mutated BdCOMT6 protein was still functional. Such a moderate down-regulation of lignin-related COMT enzyme reduced the straw recalcitrance to saccharification, without compromising the vegetative or reproductive development of the plant.